Molecular analysis of a fibrin-degrading enzyme from Bacillus subtilis K2 isolated from the Indonesian soybean-based fermented food moromi

Syahbanu, Fathma; Giriwono, Puspo Edi; Tjandrawinata, Raymond R.; Suhartono, Maggy Thenawidjaja

doi:10.1007/s11033-020-05898-2

Cited by 16 publications

(20 citation statements)

References 44 publications

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“…Our earlier work has shown that the Subtilisin K2 enzyme of Indonesian moromi is capable of hydrolyzing fibrin, as shown Molecular docking of Subtilisin K2, a fibrin-degrading enzyme from Indonesian moromi, with its substrates by the fibrin plate assay (Syahbanu et al, 2020a), as well as hydrolyzing fibrinogen in fibrinogen zymogram analysis (Syahbanu et al, 2020b). The present bioinformatic work was carried out to elucidate in more detail the mode of this interaction with the substrates fibrin and fibrinogen.…”

Section: Introductionmentioning

confidence: 83%

“…Subtilisin K2 consists of 262 amino acids, and the sequence data were saved in the FASTA format. The 3D structure of Subtilisin K2 was constructed using the SWISS-MODEL Workspace (Swiss Institute of Bioinformatics, 2020) program (RRID:SCR_018123) (Schwede et al, 2003;Arnold et al, 2006;Benkert et al, 2011;Biasini et al, 2014) as reported by Syahbanu et al (2020b). The fibrin and fibrinogen structures were retrieved from RCSB PDB (PDB IDs: 2HLO (fibrin) and 3GHG (fibrinogen)) as receptors for the molecular docking experiments with Subtilisin K2 as a ligand.…”

Section: Methodsmentioning

confidence: 99%

“…Our previous study revealed that Subtilisin K2 possesses active site residues Asp19, His51, and Ser208, which are typical of the serine protease family (Syahbanu et al, 2020b). Preliminary bioinformatic analysis suggested that Subtilisin K2 interacts with Leu168, Ile171, and Leu172 of fibrin substrates with high binding affinity (ΔG = -19.4 kcal/mol) (Syahbanu et al, 2020b). In this study, we further analyzed the interactions that occur between the enzyme and several domains of the fibrin substrate and fibrinogen substrate.…”

Section: Introductionmentioning

confidence: 94%

“…The three-dimensional model of the Subtilisin K2 protease from Bacillus subtilis K2 was developed by using the SWISS-MODEL Workspace (Schwede et al, 2003;Arnold et al, 2006;Benkert et al, 2011;Biasini et al, 2014). Our previous study revealed that Subtilisin K2 possesses active site residues Asp19, His51, and Ser208, which are typical of the serine protease family (Syahbanu et al, 2020b). Preliminary bioinformatic analysis suggested that Subtilisin K2 interacts with Leu168, Ile171, and Leu172 of fibrin substrates with high binding affinity (ΔG = -19.4 kcal/mol) (Syahbanu et al, 2020b).…”

Section: Introductionmentioning

confidence: 99%

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Molecular docking of Subtilisin K2, a fibrin-degrading enzyme from Indonesian moromi, with its substrates

et al. 2022

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Fibrinogen supplies the primary building block of the blood clot or thrombus after α-thrombin converts fibrinogen to fibrin during the final phases of coagulation. When the homeostasis system is disrupted, blood clots that aggregate in the blood vessels can lead to thrombosis. Fibrin-degrading enzyme from Bacillus subtilis K2 (Subtilisin K2) of Indonesian moromi has many excellent characteristics apart from its strong fibrinolytic activity. Bioinformatic analysis using the CDART webserver indicated that the enzyme appeared to share a conserved domain with the peptidase s8 superfamily also known as the subtilase family. This study used molecular docking between these fibrin-degrading enzymes and specific substrates (fibrin and fibrinogen) using the HADDOCK webserver and aimed to predict the enzyme mechanism of action. This analysis revealed that the enzyme interlocked with the two substrates; however, it suggested no productive interactions between Subtilisin K2 and fibrinogen. A hydrolysis reaction is suggested between Subtilisin K2 and the fibrin substrate. There was a strong indication that amino acids Asp19, His51, and Ser208 in Subtilisin K2's active site interacts with Leu168, Ile171, and Leu172 of the fibrin substrate with a ∆G of -19.4 kcal/mol. Subtilisin K2 tends to act more as a fibrin-degrading enzyme than as a fibrinogen-degrading enzyme.

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Section: Introductionmentioning

confidence: 83%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

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Molecular docking of Subtilisin K2, a fibrin-degrading enzyme from Indonesian moromi, with its substrates

et al. 2022

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“…For its use as a probiotic strain, the ingested bacteria must face the challenge of acidic environment and toxic compounds like bile during the passage through the gastrointestinal tract. B. subtilis is generally known as a neutrophile, but it also induces physiological systems that increase survival in extreme acidic conditions [28]. These systems include upregulation of dehydrogenases, decarboxylases, and SigX extracytoplasmic stress regulon.…”

Section: Functional Analysis Of Potential Probioticsmentioning

confidence: 99%

Comparative Genomic and Functional Evaluations of Bacillus subtilis Newly Isolated from Korean Traditional Fermented Foods

Choi

Shin

et al. 2020

Foods

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Many fermented foods are known to have beneficial effects on human and animal health, offering anti-aging and immunomodulatory benefits to host. Microorganisms contained in the fermented foods are known to provide metabolic products possibly improving host health. However, despite of a number of studies on the functional effects of the fermented foods, isolation and identification of the effective bacterial strains in the products are still in progress. The objective of this study was to isolate candidate functional strains in various Korean traditional fermented foods, including ganjang, gochujang, doenjang, and jeotgal, and evaluate their beneficial effects on the host, using Caenorhabditis elegans as a surrogate animal model. Among the 30 strains isolated, five Bacillus spp. were selected that increased the expression level of pmk-1, an innate immune gene of C. elegans. These strains extended the nematode lifespan and showed intestinal adhesion to the host. Based on the bioinformatic analyses of whole genome sequences and pangenomes, the five strains of Bacillus subtilis were genetically different from the strains found in East Asian countries and previously reported strains isolated from Korean fermented foods. Our findings suggest that the newly isolated B. subtilis strains can be a good candidate for probiotic with further in-depth investigation on health benefits and safety.

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Production, purification, and functional properties of microbial fibrinolytic enzymes produced by microorganism obtained from soy-based fermented foods: developments and challenges

Yao

Yang

Fan

et al. 2022

Critical Reviews in Food Science and Nutrition

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Molecular analysis of a fibrin-degrading enzyme from Bacillus subtilis K2 isolated from the Indonesian soybean-based fermented food moromi

Cited by 16 publications

References 44 publications

Molecular docking of Subtilisin K2, a fibrin-degrading enzyme from Indonesian moromi, with its substrates

Molecular docking of Subtilisin K2, a fibrin-degrading enzyme from Indonesian moromi, with its substrates

Comparative Genomic and Functional Evaluations of Bacillus subtilis Newly Isolated from Korean Traditional Fermented Foods

Production, purification, and functional properties of microbial fibrinolytic enzymes produced by microorganism obtained from soy-based fermented foods: developments and challenges

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